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Self-Correction Distillation for Structured Data Question Answering

arXiv:2511.07998v1 Announce Type: cross Abstract: Structured data question answering (QA), including table QA, Knowledge Graph (KG) QA, and temporal KG QA, is a pivotal research area. Advances in large language models (LLMs) have driven significant progress in unified structural QA frameworks like TrustUQA. However, these frameworks face challenges when applied to small-scale LLMs since small-scale LLMs are prone to errors in generating structured queries. To improve the structured data QA ability of small-scale LLMs, we propose a self-correction distillation (SCD) method. In SCD, an error prompt mechanism (EPM) is designed to detect errors and provide customized error messages during inference, and a two-stage distillation strategy is designed to transfer large-scale LLMs' query-generation and error-correction capabilities to small-scale LLM. Experiments across 5 benchmarks with 3 structured data types demonstrate that our SCD achieves the best performance and superior generalization on small-scale LLM (8B) compared to other distillation methods, and closely approaches the performance of GPT4 on some datasets. Furthermore, large-scale LLMs equipped with EPM surpass the state-of-the-art results on most datasets.

Organoids in Genetic Disorders: from Disease Modeling to Translational Applications

Stem Cell Rev Rep. 2025 Sep 11. doi: 10.1007/s12015-025-10973-x. Online ahead of print.

ABSTRACT

The emergence of organoid models has significantly bridged the gap between traditional cell cultures/animal models and authentic human disease states, particularly for genetic disorders, where their inherent genetic fidelity enables more biologically relevant research directions and enhances translational validity. This review systematically analyzes established organoid models of genetic diseases across organs (e.g., brain, eye, kidney, lung, and heart), highlighting their pivotal roles in identifying novel pathogenic genes, elucidating disease mechanisms, and advancing therapeutic strategies such as drug screening platforms, gene-editing therapies, and organ transplantation strategies. Furthermore, we critically address current limitations-including challenges in recapitulating complex pathologies and scaling production-while underscoring their potential for personalized medicine through multi-omics integration and bioengineering innovations. Although the scope of "genetic diseases" is broad, this synthesis focuses on disorders with well-defined inheritance patterns, such as monogenic disorders, copy number variations (CNVs), and aneuploidies. Despite covering only a subset of these conditions, this review aims to provide researchers with a comprehensive overview of the field, emphasizing how organoid-based approaches could accelerate both mechanistic discoveries and clinical translation in genetic disease research.

PMID:40931310 | DOI:10.1007/s12015-025-10973-x

Thor: a platform for cell-level investigation of spatial transcriptomics and histology

Nat Commun. 2025 Aug 5;16(1):7178. doi: 10.1038/s41467-025-62593-1.

ABSTRACT

Spatial transcriptomics links gene expression with tissue morphology, however, current tools often prioritize genomic analysis, lacking integrated image interpretation. To address this, we present Thor, a comprehensive platform for cell-level analysis of spatial transcriptomics and histological images. Thor employs an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptome from spot-level data, effectively combining gene expression and cell morphology. The platform includes 10 modular tools for genomic and image-based analysis, and is paired with Mjolnir, a web-based interface for interactive exploration of gigapixel images. Thor is validated on simulated data and multiple spatial platforms (ISH, MERFISH, Xenium, Stereo-seq). Thor characterizes regenerative signatures in heart failure, screens breast cancer hallmarks, resolves fine layers in mouse olfactory bulb, and annotates fibrotic heart tissue. In high-resolution Visium HD data, it enhances spatial gene patterns aligned with histology. By bridging transcriptomic and histological analysis, Thor enables holistic tissue interpretation in spatial biology.

PMID:40764306 | PMC:PMC12325965 | DOI:10.1038/s41467-025-62593-1

Purine salvage–associated metabolites as biomarkers for early diagnosis of esophageal squamous cell carcinoma: a diagnostic model–based study

Cell Death Discovery, Published online: 14 March 2024; doi:10.1038/s41420-024-01896-6

Purine salvage–associated metabolites as biomarkers for early diagnosis of esophageal squamous cell carcinoma: a diagnostic model–based study

Hypermethylation of tumor suppressor lncRNA MEF2C-AS1 frequently happened in patients at all stages of colorectal carcinogenesis

The novel long noncoding RNA MEF2C-AS1 has been identified to play suppressor roles during tumorigenesis. DNA methylation has a regulatory effect on gene expression in cancer initiation and progression. However, ...
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